Example I/O of FIRM.
Full Iterative Relaxation Matrix
mode=0 -> manual mode=1 -> auto merging of NOEs
mode=2 -> manual restart mode=3 -> auto merging restart
enter mode: 0
mixing time: 0.3
correlation time: 2e-9
methyl N-site jump (0,3,6,12): 3
methyl correlation time: 5e-11
additional leakage relaxation: 0
PDB coord file: example2.pdb
experimental NOEs: example.noe
calibration file for scaling ( for all NOEs):
sub model rates back in during refinement? (-/n):
output distance file: temp3.dis
output NOE file:
total number of protons = 25
number of methyl rotors = 1
equivalent aromatic proton-pairs = 2
calculating model NOE matrix ...
scaled to all measured NOEs
scaling factor for experimental NOEs: 0.9629
NOEs with largest fractional deviation: (calc exp dev)
HN GLU 4 HG2 GLU 4 0.0650 0.0049 12.239
HN THR 1 HG1 THR 1 0.0705 0.0074 8.510
HN THR 1 HG2 THR 1 0.0705 0.0074 8.510
HN THR 1 HG3 THR 1 0.0705 0.0074 8.510
HN GLU 4 HG3 GLU 4 0.0338 0.0056 5.045
noe Rfactor numer/denom: 0.1854E+01 / 0.4302E+01
noe Rfactor = 0.4309 r Rfactor = 0.1327 deviation = 0.8562
>1 write output and continue
<0 write output and exit
=0 exit
FRACTION OF EXPERIMENTAL NOEs TO MERGE: 1
back calculation: get new rates from merged NOEs ...
make new diagonal from sum of cross peaks ...
make new NOE matrix from relaxation matrix ...
scaling factor for experimental NOEs: 0.9833
NOEs with largest fractional deviation: (calc exp dev)
HA THR 1 HG2 GLU 4 0.0020 0.0032 0.385
HN TYR 2 HD2 TYR 2 0.0863 0.1107 0.220
HN TYR 2 HD1 TYR 2 0.0865 0.1108 0.219
HN THR 1 HB THR 1 0.0591 0.0489 0.207
HA THR 1 HN TYR 2 0.0179 0.0216 0.170
noe Rfactor numer/denom: 0.3028E+00 / 0.4230E+01
noe Rfactor = 0.0716 r Rfactor = 0.0115 deviation = 0.0686
>1 write output and continue
<0 write output and exit
=0 exit
FRACTION OF EXPERIMENTAL NOEs TO MERGE: -1
writing output ...
program end.
Example Output Distance File
mixing time= 0.300
real/pseudo-distances calc model calcNOE expNOE deviation
HN THR 1 HA THR 1 2.208 2.926 0.1606 0.1465 0.0396
HN THR 1 HB THR 1 2.734 2.800 0.0591 0.0489 0.1019
HN THR 1 HG1 THR 1 3.980 3.005 0.0080 0.0073 0.0627
HN THR 1 HG2 THR 1 3.980 3.479 0.0080 0.0073 0.0627
HN THR 1 HG3 THR 1 3.980 1.852 0.0080 0.0073 0.0627
HN THR 1 HN TYR 2 2.995 3.935 0.0221 0.0231 -0.0252
HN THR 1 HD1 TYR 2 3.726 2.769 0.0101 0.0099 0.0072
HN THR 1 HE1 TYR 2 4.569 4.015 0.0033 0.0029 0.1064
HN THR 1 HE2 TYR 2 4.569 7.572 0.0033 0.0029 0.1093
HN THR 1 HD2 TYR 2 3.726 7.012 0.0100 0.0099 0.0064
HA THR 1 HN TYR 2 3.103 3.188 0.0179 0.0216 -0.1191
HA THR 1 HA TYR 2 5.222 5.073 0.0028 0.0032 -0.1122
HA THR 1 HB2 TYR 2 4.487 4.873 0.0034 0.0032 0.0382
HA THR 1 HD1 TYR 2 4.460 4.212 0.0057 0.0062 -0.0646
... etc ...
Return to FIRM Documentation